Process Chart for Controlling Wafer Defects using Fuzzy Theory

Manufacturers of integrated circuits (IC) frequently utilize c-charts to monitor wafer defects. The clustering of wafer defects increases with the surface area of the wafers. The clustering of defects causes the Poisson-based c-chart to show many false alarms. Although Neyman-based c-chart has been developed to reduce the number of false alarms, it has some shortcomings in practical use. This study presents a process control chart that applies Fuzzy theory and the engineering experience to monitor the clustered defects on a wafer. The proposed method is simpler and more efficient than that of the Neyman-based c-chart. A case study of an IC company in Taiwan demonstrates the effectiveness of the proposed method

iTAR: A Web Server for Identifying Target Genes of Transcription Factors using ChIP-Seq or ChIP-Chip Data

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP’s output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server (http://syslab3.nchu.edu.tw/iTAR/) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF

Adaptive Optimization Algorithm for Resetting Techniques in Obstacle-ridden Environments

Redirected Walking (RDW) algorithms aim to impose several types of gains on users immersed in Virtual Reality and distort their walking paths in the real world, thus enabling them to explore a larger space. Since collision with physical boundaries is inevitable, a reset strategy needs to be provided to allow users to reset when they hit the boundary. However, most reset strategies are based on simple heuristics by choosing a seemingly suitable solution, which may not perform well in practice. In this paper, we propose a novel optimization-based reset algorithm adaptive to different RDW algorithms. Inspired by the approach of finite element analysis, our algorithm splits the boundary of the physical world by a set of endpoints. Each endpoint is assigned a reset vector to represent the optimized reset direction when hitting the boundary. The reset vectors on the edge will be determined by the interpolation between two neighbouring endpoints. We conduct simulation-based experiments for three RDW algorithms with commonly used reset algorithms to compare with. The results demonstrate that the proposed algorithm significantly reduces the number of resets.</p

Genome-wide gene-based association study

Genome-wide association studies, which analyzes hundreds of thousands of single-nucleotide polymorphisms to identify disease susceptibility genes, are challenging because the work involves intensive computation and complex modeling. We propose a two-stage genome-wide association scanning procedure, consisting of a single-locus association scan for the first stage and a gene-based association scan for the second stage. Marginal effects of single-nucleotide polymorphisms are examined by using the exact Armitage trend test or logistic regression, and gene effects are examined by using a p-value combination method. Compared with some existing single-locus and multilocus methods, the proposed method has the following merits: 1) convenient for definition of biologically meaningful regions, 2) powerful for detection of minor-effect genes, 3) helpful for alleviation of a multiple-testing problem, and 4) convenient for result interpretation. The method was applied to study Genetic Analysis Workshop 16 Problem 1 rheumatoid arthritis data, and strong association signals were found. The results show that the human major histocompatibility complex region is the most important genomic region associated with rheumatoid arthritis. Moreover, previously reported genes including PTPN22, C5, and IL2RB were confirmed; novel genes including HLA-DRA, BTNL2, C6orf10, NOTCH4, TAP2, and TNXB were identified by our analysis

Nanocomposites of Tantalum-Based Pyrochlore and Indium Hydroxide Showing High and Stable Photocatalytic Activities for Overall Water Splitting and Carbon Dioxide Reduction

Nanocomposites of tantalum-based pyrochlore nanoparticles and indium hydroxide were prepared by a hydrothermal process for UV-driven photocatalytic reactions including overall water splitting, hydrogen production from photoreforming of methanol, and CO_2 reduction with water to produce CO. The best catalyst was more than 20 times more active than sodium tantalate in overall water splitting and 3 times more active than Degussa P25 TiO_2 in CO_2 reduction. Moreover, the catalyst was very stable while generating stoichiometric products of H_2 (or CO) and O_2 throughout long-term photocatalytic reactions. After the removal of In(OH)_3, the pyrochlore nanoparticles remained highly active for H_2 production from pure water and aqueous methanol solution. Both experimental studies and density functional theory calculations suggest that the pyrochlore nanoparticles catalyzed the water reduction to produce H2, whereas In(OH)_3 was the major active component for water oxidation to produce O_2

Photopolymerizable Hydrogel-Encapsulated Fibromodulin-Reprogrammed Cells for Muscle Regeneration

A central challenge in tissue engineering is obtaining a suitable cell type with a capable delivery vehicle to replace or repair damaged or diseased tissues with tissue mimics. Notably, for skeletal muscle tissue engineering, given the inadequate availability and regenerative capability of endogenous myogenic progenitor cells as well as the tumorigenic risks presented by the currently available pluri- and multipotent stem cells, seeking a safe regenerative cell source is urgently demanded. To conquer this problem, we previously established a novel reprogramming technology that can generate multipotent cells from dermal fibroblasts using a single protein, fibromodulin (FMOD). The yield FMOD-reprogrammed (FReP) cells exhibit exceeding myogenic capability without tumorigenic risk, making them a promising and safe cell source for skeletal muscle establishment. In addition to using the optimal cell for implantation, it is equally essential to maintain cellular localization and retention in the recipient tissue environment for critical-sized muscle tissue establishment. In this study, we demonstrate that the photopolymerizable methacrylated glycol chitosan (MeGC)/type I collagen (ColI)hydrogel provides a desirable microenvironment for encapsulated FReP cell survival, spreading, extension, and formation of myotubes in the hydrogel three-dimensionally in vitro, without undesired osteogenic, chondrogenic, or tenogenic differentiation. Furthermore, gene profiling revealed a paired box 7 (PAX7) / myogenic factor 5 (MYF5) / myogenic determination 1 (MYOD1) / myogenin (MYOG) / myosin cassette elevation in the encapsulated FReP cells during myogenic differentiation, which is similar to that of the predominant driver of endogenous skeletal muscle regeneration, satellite cells. These findings constitute the evidence that the FReP cell-MeGC/ColI-hydrogel construct is a promising tissue engineering mimic for skeletal muscle generation in vitro, and thus possesses the extraordinary potential for further in vivo validation. © 2020 Mary Ann Liebert Inc.. All rights reserved

Inferring Condition-Specific Targets of Human TF-TF Complexes Using ChIP-seq Data

Background: Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes. Results: Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted 2,392 TF complexes and 13,504 high-confidence or 127,994 low-confidence regulatory interactions amongst TF complexes and their target genes. We validated our predictions by (i) comparing predicted TF complexes to external TF complex databases, (ii) validating selected target genes of TF complexes using ChIP-qPCR and RT-PCR experiments, and (iii) analysing target genes of select TF complexes using gene ontology enrichment to demonstrate the accuracy of our work. Finally, the predicted results above were integrated and employed to construct a CST database. Conclusions: We built up a methodology to construct the CST database, which contributes to the analysis of transcriptional regulation and the identification of novel TF-TF complex formation in a certain condition. This database also allows users to visualize condition-specific TF regulatory networks through a user-friendly web interface

Inferring Condition-Specific Targets of Human TF-TF Complexes Using ChIP-seq Data

Background: Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes. Results: Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted 2,392 TF complexes and 13,504 high-confidence or 127,994 low-confidence regulatory interactions amongst TF complexes and their target genes. We validated our predictions by (i) comparing predicted TF complexes to external TF complex databases, (ii) validating selected target genes of TF complexes using ChIP-qPCR and RT-PCR experiments, and (iii) analysing target genes of select TF complexes using gene ontology enrichment to demonstrate the accuracy of our work. Finally, the predicted results above were integrated and employed to construct a CST database. Conclusions: We built up a methodology to construct the CST database, which contributes to the analysis of transcriptional regulation and the identification of novel TF-TF complex formation in a certain condition. This database also allows users to visualize condition-specific TF regulatory networks through a user-friendly web interface

Temporal and Spatial Variations in spatial variations in symbiont communities of catch bowl coral Isopora palifera (Scleractinia: Acroporidae) on reefs in Kenting National Park, Taiwan

Acclimatization through Symbiodinium shuffling is one of potential mechanisms in reef-building corals to survive environmental stress. In our previous study, the catch bowl coral Isopora palifera in Tantzei Bay (TZB), Nanwan, Kenting National Park (KNP), southern Taiwan was demonstrated to shuffle thermal-tolerant Symbiodinium D1a and thermal-sensitive Symbiodinium C3 in response to seasonal variations in sea surface temperatures (SSTs) in 2000 and 2001. In this study, we reexamined the temporal dynamics of the Symbiodinium community of I. palifera in TZB in 2006-2009. In addition, spatial variations in Symbiodinium communities in I. palifera were also examined at 6 other sites of Nanwan, KNP in 2009, including a site located at a nuclear power plant outlet (NPP-OL) in southern Taiwan with a yearly mean SST 0.6-1.5 degrees C higher compared to the other sites. Phylotyping and DNA sequence analyses of Symbiodinium ribosomal 28S and ITS2 markers showed that I. palifera colonies at TZB continued to show seasonal shuffling, but shifted to thermal-sensitive type C3 dominant in 2006-2009. This differed from the symbiont community originally dominated by the thermal-tolerant Symbiodinium D1a in 2000 and 2001 after the 1998 mass-bleaching event. Significant differences in spatial variations of the symbiont community in Nanwan were detected with I. palifera colonies at the NPP-OL dominated by Symbiodinium D1a. Our study results suggest that I. palifera can acclimatize to SST anomalies by shuffling to thermal-tolerant Symbiodinium D1a and can revert to thermal-sensitive C3 when the stress disappears, but will maintain the thermally tolerant Symbiodinium D1a as the dominant symbiont if the heat stress continues